[Stacomir-commits] r403 - in pkg/stacomir: R data inst/config man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jun 20 14:43:27 CEST 2017
Author: briand
Date: 2017-06-20 14:43:27 +0200 (Tue, 20 Jun 2017)
New Revision: 403
Added:
pkg/stacomir/man/coef_durif.Rd
Removed:
pkg/stacomir/man/coef_Durif.Rd
Modified:
pkg/stacomir/R/data.R
pkg/stacomir/R/fungraph.R
pkg/stacomir/R/fungraph_glasseel.R
pkg/stacomir/R/interface_report_mig_char.R
pkg/stacomir/R/ref_dc.R
pkg/stacomir/R/ref_df.R
pkg/stacomir/R/ref_env.R
pkg/stacomir/R/ref_par.R
pkg/stacomir/R/ref_period.R
pkg/stacomir/R/ref_stage.R
pkg/stacomir/R/ref_taxa.R
pkg/stacomir/R/ref_timestep_daily.R
pkg/stacomir/R/ref_year.R
pkg/stacomir/R/report_annual.R
pkg/stacomir/R/report_dc.R
pkg/stacomir/R/report_df.R
pkg/stacomir/R/report_env.R
pkg/stacomir/R/report_ge_weight.R
pkg/stacomir/R/report_mig.R
pkg/stacomir/R/report_mig_char.R
pkg/stacomir/R/report_mig_interannual.R
pkg/stacomir/R/report_mig_mult.R
pkg/stacomir/R/report_sample_char.R
pkg/stacomir/R/report_sea_age.R
pkg/stacomir/R/report_silver_eel.R
pkg/stacomir/R/stacomi.R
pkg/stacomir/R/utilities.R
pkg/stacomir/data/r_mig_char.rda
pkg/stacomir/inst/config/libraries.r
pkg/stacomir/inst/config/stacomi_checks.R
pkg/stacomir/inst/config/stacomi_manual_launch.r
pkg/stacomir/man/calcule-report_mig-method.Rd
pkg/stacomir/man/calcule-report_mig_interannual-method.Rd
pkg/stacomir/man/calcule-report_mig_mult-method.Rd
pkg/stacomir/man/charge-ref_year-method.Rd
pkg/stacomir/man/charge-report_env-method.Rd
pkg/stacomir/man/choice_c-ref_dc-method.Rd
pkg/stacomir/man/choice_c-ref_df-method.Rd
pkg/stacomir/man/choice_c-ref_env-method.Rd
pkg/stacomir/man/choice_c-ref_par-method.Rd
pkg/stacomir/man/choice_c-ref_stage-method.Rd
pkg/stacomir/man/choice_c-ref_taxa-method.Rd
pkg/stacomir/man/choice_c-ref_timestep_daily-method.Rd
pkg/stacomir/man/choice_c-report_sea_age-method.Rd
pkg/stacomir/man/colortable.Rd
pkg/stacomir/man/connect-report_annual-method.Rd
pkg/stacomir/man/connect-report_mig_interannual-method.Rd
pkg/stacomir/man/funchartDC.Rd
pkg/stacomir/man/funchartDF.Rd
pkg/stacomir/man/fungraph.Rd
pkg/stacomir/man/fungraph_glasseel.Rd
pkg/stacomir/man/funtablereport_sample_char.Rd
pkg/stacomir/man/funtablereport_sea_age.Rd
pkg/stacomir/man/funtablereport_silver_eel.Rd
pkg/stacomir/man/graphdate.Rd
pkg/stacomir/man/graphe-methods.Rd
pkg/stacomir/man/h_report_mig_mult_graph.Rd
pkg/stacomir/man/h_report_mig_multgraph3.Rd
pkg/stacomir/man/hbmCcalc.Rd
pkg/stacomir/man/hbmCstat.Rd
pkg/stacomir/man/hgraph_report_mig_interannual4.Rd
pkg/stacomir/man/hgraph_report_mig_interannual5.Rd
pkg/stacomir/man/interface_report_species.Rd
pkg/stacomir/man/plot-report_mig-ANY-method.Rd
pkg/stacomir/man/plot-report_mig_interannual-missing-method.Rd
pkg/stacomir/man/plot-report_mig_mult-missing-method.Rd
pkg/stacomir/man/quitte.Rd
pkg/stacomir/man/r_ann_adour.Rd
pkg/stacomir/man/r_mig_char.Rd
pkg/stacomir/man/ref_dc-class.Rd
pkg/stacomir/man/ref_par-class.Rd
pkg/stacomir/man/ref_parqual-class.Rd
pkg/stacomir/man/ref_period-class.Rd
pkg/stacomir/man/ref_timestep_daily-class.Rd
pkg/stacomir/man/report_dc-class.Rd
pkg/stacomir/man/report_df-class.Rd
pkg/stacomir/man/report_ge_weight-class.Rd
pkg/stacomir/man/report_silver_eel-class.Rd
pkg/stacomir/man/stacomiR-package.Rd
pkg/stacomir/man/write_database-report_sea_age-method.Rd
pkg/stacomir/man/xtable-report_annual-method.Rd
pkg/stacomir/man/xtable-report_mig_char-method.Rd
Log:
Finall spell checks
Modified: pkg/stacomir/R/data.R
===================================================================
--- pkg/stacomir/R/data.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/data.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -257,7 +257,7 @@
#' Annual migration of salmon in the Adour and tributaries
#'
#' The dataset corresponds to the fishways DC=33:40 of the Adour for adult migrant salmons
-#' from 1996 to 2005 (annual counts). It has been kinly provided as an example set by the Migradour
+#' from 1996 to 2005 (annual counts). It has been kindly provided as an example set by the Migradour
#' association.
#' @format An object of class \link{report_annual-class} with data slot loaded.
#' @keywords data
@@ -397,7 +397,7 @@
#' Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)
#'
-#' The dataset corresponds to the caracteristics (qualitative and quantitative) of salmo salar migrating
+#' The dataset corresponds to the characteristics (qualitative and quantitative) of salmo salar migrating
#' at Decize (Loire river) and Vichy (Allier river) counting device in 2012. It has been loaded as
#' an example for the report_mig_char-class and kindly provided by Loire Grands Migrateurs (LOGRAMI).
#' @format An object of class \link{report_mig_char-class} with data slot loaded:
Modified: pkg/stacomir/R/fungraph.R
===================================================================
--- pkg/stacomir/R/fungraph.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/fungraph.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -1,4 +1,4 @@
-#' Function for report_mig graphes including numbers DF DC operations
+#' Function for report_mig graphs including numbers DF DC operations
#'
#' This graph is for species other than glass eel
#'
@@ -192,7 +192,7 @@
cex=cex+0.2)
###################################
- # temps de fonctionnement du DF
+ # time for DF (fishway) operation
###################################
if (dim(report_df at data)[1]==0 ) {
@@ -294,7 +294,7 @@
cex=cex+0.2
)
###################################
- # temps de fonctionnement du DC
+ # time for DC (counting device) operation
###################################
Modified: pkg/stacomir/R/fungraph_glasseel.R
===================================================================
--- pkg/stacomir/R/fungraph_glasseel.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/fungraph_glasseel.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -14,7 +14,7 @@
#' @param dc the counting device, default to null, only necessary for \link{report_mig_mult-class}
#' @param silent Message displayed or not
#' @param color Default NULL, a vector of length 11 of color in the following order, numbers, weight, working, stopped, 1...5 types of operation,
-#' the 2 latest colors are not used but keeped for consistency with fungraph
+#' the 2 latest colors are not used but kept for consistency with fungraph
#' for the fishway, if null will be set to brewer.pal(12,"Paired")[c(4,6,1,2,3,5,7,8,10,11,12)]
#' @param color_ope Default NULL, a vector of color for the operations. Default to brewer.pal(4,"Paired")
#' @param ... additional parameters passed to plot, main, ylab, cex.main, font.main, type, xlim, ylim, lty, bty, pch
@@ -70,7 +70,7 @@
eff.p=table$Effectif_total.p
debut=unclass(as.Date(time.sequence[min(index)]))[[1]]
fin=unclass(as.Date(time.sequence[max(index)]))[[1]]
- eff[eff==0]<-NA #pour les besoins du graphe
+ eff[eff==0]<-NA #for graph need
eff.p[eff.p==0]<-NA
dis_commentaire= as.character(report_mig at dc@data$dis_commentaires[report_mig at dc@data$dc%in%dc])
if (!silent) funout(gettextf("Glass eels graph %s\n",dis_commentaire))
@@ -220,7 +220,7 @@
cex=cex+0.2)
###################################
- # temps de fonctionnement du DF
+ # Time for dc operation
###################################
if (dim(report_df at data)[1]==0 ) {
@@ -322,7 +322,7 @@
bty="n",
cex=cex+0.2)
###################################
- # temps de fonctionnement du DC
+ # time for DC (counting device) operation
###################################
Modified: pkg/stacomir/R/interface_report_mig_char.R
===================================================================
--- pkg/stacomir/R/interface_report_mig_char.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/interface_report_mig_char.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -8,7 +8,7 @@
r_mig_char=new("report_mig_char")
assign("r_mig_char",r_mig_char,envir=envir_stacomi)
- report_dc=new("report_dc") # appel ici pour pouvoir utiliser les fonctions graphiques associees sur fonctionnement du DC
+ report_dc=new("report_dc")
assign("report_dc",report_dc,envir=envir_stacomi)
objectreport="r_mig_char"
Modified: pkg/stacomir/R/ref_dc.R
===================================================================
--- pkg/stacomir/R/ref_dc.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_dc.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -6,7 +6,7 @@
#' @slot dc_selectionne Object of class \code{"integer"}, The selected device
#' @slot ouvrage Object of class \code{"integer"}, the attached dam
#' @slot station Object of class \code{"character"}, the attached migration monitoring station, this is necessary to join the
-#' table of escapments calculated at the station level.
+#' table of escapements calculated at the station level.
#' @slot data Object of class \code{"data.frame"} data pertaining to the control device
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("ref_dc", dc_selectionne=integer(), ouvrage=integer(),
@@ -295,7 +295,7 @@
#' Command line interface to select a counting device
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line. The parameters for dc are transformed to integer as the ref_dc only
#' takes integer in the dc slots. The method also loads the stations and ouvrages (dams) associated with the counting device (dc).
#' The values passed to the choice_c method are then checked with the setValidty method.
Modified: pkg/stacomir/R/ref_df.R
===================================================================
--- pkg/stacomir/R/ref_df.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_df.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -113,7 +113,7 @@
#' Command line interface to choose a fishway
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line. The parameters for dF are transformed to integer as the ref_df only
#' takes integer in the df slots.
#' DF are third in hierarchy in the stacomi database Station>ouvrage>DF>DC>operation. This class is only used in the
Modified: pkg/stacomir/R/ref_env.R
===================================================================
--- pkg/stacomir/R/ref_env.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_env.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -86,7 +86,7 @@
#' Command line interface to select a monitoring station
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line.
#' @param object an object of class ref_env
#' @param stationMesure a character vector of the monitoring station code (corresponds to stm_libelle in the tj_stationmesure_stm table)
Modified: pkg/stacomir/R/ref_par.R
===================================================================
--- pkg/stacomir/R/ref_par.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_par.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -132,7 +132,7 @@
#' Command line interface to select a parameter
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line.
#' If an objectreport is passed as a parameter, the method will do a charge_with_filter to select only the taxa present in the counting devices
#' @param object an object of class \link{ref_par-class}
Modified: pkg/stacomir/R/ref_period.R
===================================================================
--- pkg/stacomir/R/ref_period.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_period.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -8,7 +8,7 @@
#' @section Objects from the Class: Objects can be created by calls of the form
#' \code{new("ref_period", ...)}.
#' @keywords classes
-#' @slot data="data.frame" providing correspondance between period and their english names
+#' @slot data="data.frame" providing correspondance between period and their English names
#' @family referential objects
setClass(Class="ref_period",representation=
representation(
Modified: pkg/stacomir/R/ref_stage.R
===================================================================
--- pkg/stacomir/R/ref_stage.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_stage.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -302,7 +302,7 @@
#' choice_c method for ref_stage
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line. The values passed to the choice_c method
#' for stage is the code. Any numeric value will be discarded
#' @param object An object of class \link{ref_stage-class}
Modified: pkg/stacomir/R/ref_taxa.R
===================================================================
--- pkg/stacomir/R/ref_taxa.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_taxa.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -219,7 +219,7 @@
#' choice_c method for ref_taxa
#'
-#' the choice_cc method is intented to have the same behaviour as choice (which creates a
+#' the choice_cc method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line. The values passed to the choice_c method
#' for taxa can be either numeric (2038 = Anguilla anguilla) or character.
#' @param object An object from the class ref_taxa
Modified: pkg/stacomir/R/ref_timestep_daily.R
===================================================================
--- pkg/stacomir/R/ref_timestep_daily.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_timestep_daily.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -18,7 +18,7 @@
#' Class "ref_timestep_daily"
#'
#' Representation of a ref_timestep object with a step length equal to one day.
-#' It receives an heritance from ref_timestep
+#' It receives an inheritance from ref_timestep
#'
#' validite_ref_timestep_daily
#' @include ref_timestep.R
@@ -98,7 +98,7 @@
#' choice_c method for class ref_timestep_daily
#'
-#' the choice_c method is intented to have the same behaviour as choice (which creates a
+#' the choice_c method is intendedto have the same behaviour as choice (which creates a
#' widget in the graphical interface) but from the command line.
#' @param object An object of class \link{ref_timestep_daily-class}
#' @param datedebut A character (format \code{"15/01/1996"} or \code{"1996-01-15"} or \code{"15-01-1996"}), or POSIXct object
Modified: pkg/stacomir/R/ref_year.R
===================================================================
--- pkg/stacomir/R/ref_year.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/ref_year.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -34,7 +34,7 @@
#' Loading method for ref_year referential objects
#'
-#' Selects year available either in the bjo table (if Objetreport==report_migInterannelle) or in the t_operation_ope table
+#' Selects year available either in the bjo table (if report_object==report_migInterannelle) or in the t_operation_ope table
#' @param object An object of class ref_year
#' @param objectreport The object report, default "report_ge_weight" other possible value report_mig_interannual
#' @return object An object of class ref_year with slot data filled with the selected value
Modified: pkg/stacomir/R/report_annual.R
===================================================================
--- pkg/stacomir/R/report_annual.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_annual.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -86,7 +86,7 @@
#' not count subsamples.
#' @param object An object of class \link{report_annual-class}
#' @param silent Stops messages from being displayed if silent=TRUE, default FALSE
-#' @return An instantianted object with values filled with user choice
+#' @return An instantiated object with values filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @return A dataframe with column effectif, comprising the sum of report_mig counts
#' @aliases connect.report_annual
@@ -229,7 +229,7 @@
return(r_ann)
})
-#' xtable funciton for \link{report_annual-class}
+#' xtable function for \link{report_annual-class}
#' create an xtable objet but also assigns an add.to.column argument in envir_stacomi,
#' for later use by the print.xtable method.
#' @param x, an object of class "report_annual"
Modified: pkg/stacomir/R/report_dc.R
===================================================================
--- pkg/stacomir/R/report_dc.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_dc.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -2,7 +2,7 @@
#' comptage
#'
#' The counting device is not always working. It may me stopped either
-#' following a monitoring protocol, or due to misfunction of the device, this
+#' following a monitoring protocol, or due to malfunction of the device, this
#' class allows to draw graphics allowing an overview of the device operation
#' @slot data A data frame
#' @slot dc An object of class \code{ref_dc-class}
@@ -169,12 +169,9 @@
funout(gettext("No data for this counting device\n",domain="R-stacomiR"),arret=TRUE)
if (plot.type=="1"|plot.type=="2"){
t_periodefonctdispositif_per=report_dc at data # on recupere le data.frame
- # l'objectif du programme ci dessous est de calculer la time.sequence mensuelle de fonctionnement du dispositif.
- tempsdebut<-t_periodefonctdispositif_per$per_date_debut
+ tempsdebut<-t_periodefonctdispositif_per$per_date_debut
tempsfin<-t_periodefonctdispositif_per$per_date_fin
- # test la premiere horodate peut etre avant le choix de temps de debut, remplacer cette date par requete at datedebut
tempsdebut[tempsdebut<report_dc at horodatedebut@horodate]<-report_dc at horodatedebut@horodate
- # id pour fin
tempsfin[tempsfin>report_dc at horodatefin@horodate]<-report_dc at horodatefin@horodate
t_periodefonctdispositif_per=cbind(t_periodefonctdispositif_per,tempsdebut,tempsfin)
seqmois=seq(from=tempsdebut[1],to=tempsfin[nrow(t_periodefonctdispositif_per)],by="month",tz = "GMT")
@@ -182,8 +179,6 @@
# adding one month at the end to get a complete coverage of the final month
seqmois<-c(seqmois,
seqmois[length(seqmois)]%m+%months(1))
-
- #seqmois<-c(seqmois,seqmois[length(seqmois)]+months(1))
t_periodefonctdispositif_per_mois=t_periodefonctdispositif_per[1,]
############################
#progress bar
@@ -478,7 +473,7 @@
plot(report_dc,plot.type=3)
}
-#' Handler fonction to plot calendar like graph, internal use
+#' Handler function to plot calendar like graph, internal use
#' @param h handler
#' @param ... additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
Modified: pkg/stacomir/R/report_df.R
===================================================================
--- pkg/stacomir/R/report_df.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_df.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -8,7 +8,7 @@
#' In the database the operation of the fishway (DF) and counting device (DC) is agregated in one table (t_periodefonctdispositif_per).
#' The column per_etat_fonctionnement indicates whether the fishway is operational (with a boolean) and the column per_tar_code indicates
#' the status of either the fishway or DC. In the database four types of operation are set, "1"=normal operation,
-#' "2"=Device stopped in nomral operation (ie lift ascending, high tide...),
+#' "2"=Device stopped in normal operation (ie lift ascending, high tide...),
#' "3"="Stopped for maintenance or other problem",
#' "4"="Works but not fully operational, ie flow problem, flood, clogged with debris...",
#' "5"="Not known")
@@ -174,12 +174,9 @@
funout(gettext("No data for this fishway\n",domain="R-stacomiR"),arret=TRUE)
if (plot.type=="1"|plot.type=="2"){
t_periodefonctdispositif_per=report_df at data # on recupere le data.frame
- # l'objectif du programme ci dessous est de calculer la time.sequence mensuelle de fonctionnement du dispositif.
tempsdebut<-t_periodefonctdispositif_per$per_date_debut
tempsfin<-t_periodefonctdispositif_per$per_date_fin
- # test la premiere horodate peut etre avant le choix de temps de debut, remplacer cette date par requete at datedebut
tempsdebut[tempsdebut<report_df at horodatedebut@horodate]<-report_df at horodatedebut@horodate
- # id pour fin
tempsfin[tempsfin>report_df at horodatefin@horodate]<-report_df at horodatefin@horodate
t_periodefonctdispositif_per=cbind(t_periodefonctdispositif_per,tempsdebut,tempsfin)
seqmois=seq(from=tempsdebut[1],to=tempsfin[nrow(t_periodefonctdispositif_per)],by="month",tz = "GMT")
@@ -456,7 +453,7 @@
}
-#' Handler fonction to plot calendar like graph, internal use
+#' Handler function to plot calendar like graph, internal use
#' @param h handler
#' @param ... additional parameters
#' @keywords internal
Modified: pkg/stacomir/R/report_env.R
===================================================================
--- pkg/stacomir/R/report_env.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_env.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -155,7 +155,6 @@
vplayout <- function(x, y) { grid::viewport(layout.pos.row = x, layout.pos.col = y) }
grid::grid.newpage()
grid::pushViewport(grid::viewport(layout = grid::grid.layout(length(unique(dat$env_stm_identifiant)),1,just="center")))
- # la liste des graphes calcules
lesGraphes=list()
if(length(unique(dat$env_stm_identifiant))!= nrow(r_env at stationMesure@data))
{
Modified: pkg/stacomir/R/report_ge_weight.R
===================================================================
--- pkg/stacomir/R/report_ge_weight.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_ge_weight.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -9,7 +9,7 @@
#' Some plots are provided to display the coefficients stored in the database, and the model results. A parameter provided in
#' the graphical interface or in the command line (slot liste) takes values "1", ">1", "tous" wich mean respectively use
#' only individual sample of glass eels, or use "group weights" which can be more close to the real weight of glass eel
-#' during counts as glass eel are not completely drained from their water during handling to preserve their muccus. The list choice
+#' during counts as glass eel are not completely drained from their water during handling to preserve their mucus. The list choice
#' "tous" means that both individual and group weights are selected.
#' @include ref_coe.R
#' @note In this class some tools are available to import glass eel measurement from
Modified: pkg/stacomir/R/report_mig.R
===================================================================
--- pkg/stacomir/R/report_mig.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_mig.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -159,7 +159,6 @@
}
if (exists("timestep",envir_stacomi)){
report_mig at timestep<-get("timestep",envir_stacomi)
- # pour permettre le fonctionnement de Fonctionnement DC
} else {
funout(gettext("Attention, no time step selected, compunting with default value\n",domain="R-stacomiR"),arret=FALSE)
warning(gettext("Attention, no time step selected, compunting with default value\n",domain="R-stacomiR"))
@@ -221,7 +220,7 @@
#' \item{contient_poids}{A boolean which indicates, in the case of glass eel, that the function \link{fun_weight_conversion} has been run to convert the weights to numbers using the weight
#' to number coefficients in the database (see link{report_ge_weight}).}
#' \item{negative}{A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers,
-#' not developped yet}}
+#' not developed yet}}
#' @aliases calcule.report_mig
#' @export
setMethod("calcule",signature=signature("report_mig"),definition=function(object,negative=FALSE,silent=FALSE){
@@ -385,8 +384,6 @@
taxa=report_mig at taxa@data[1,"tax_nom_latin"]
stage=report_mig at stage@data[1,"std_libelle"]
dc=as.numeric(report_mig at dc@dc_selectionne)[1]
- # preparation du jeu de donnees pour la fonction fungraph_civ
- #developpee pour la classe report_mig
data<-report_mig at calcdata[[stringr::str_c("dc_",dc)]][["data"]]
if (!is.null(data)){
if (nrow(data)>0){
Modified: pkg/stacomir/R/report_mig_char.R
===================================================================
--- pkg/stacomir/R/report_mig_char.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_mig_char.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -405,7 +405,7 @@
funout(gettext("You need to launch computation first, clic on calc\n",domain="R-stacomiR"),arret=TRUE)
}
}
-#' This handler calls the generic method graphe on object plot.type 3
+#' This handler calls the generic method stat
#'
#'
#' @param h handler
@@ -527,7 +527,7 @@
})
-#' xtable funciton for \link{report_mig_char-class}
+#' xtable function for \link{report_mig_char-class}
#' create an xtable objet to be later used by the print.xtable method.
#' @param x, an object of class "report_mig_char"
#' @param caption, see xtable
Modified: pkg/stacomir/R/report_mig_interannual.R
===================================================================
--- pkg/stacomir/R/report_mig_interannual.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_mig_interannual.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -49,7 +49,7 @@
setValidity("report_mig_interannual",function(object)
{
# if more than one taxa, the connect method will fail when trying to run the write_database for missing data
- # also plots have not been developped accordingly
+ # also plots have not been developed accordingly
rep1=ifelse(length(object at taxa@data$tax_code)==1,TRUE,gettext("report_migInterannuelle can only take one taxa", domain="R-stacomiR"))
# same for stage
rep2=ifelse(length(object at stage@data$std_code)==1,TRUE,gettext("report_migInterannuelle can only take one stage", domain="R-stacomiR"))
@@ -71,7 +71,7 @@
#' @param object An object of class \link{report_mig_interannual-class}
#' @param silent Stops messages from being displayed if silent=TRUE, default FALSE
#' @param check Checks that data are corresponding between report_annual and report_mig
-#' @return report_mig_interannual an instantianted object with values filled with user choice
+#' @return report_mig_interannual an instantiated object with values filled with user choice
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @aliases connect.report_mig_interannual
#' @export
@@ -371,7 +371,7 @@
report_mig_interannual at taxa<-choice_c(report_mig_interannual at taxa,taxa)
report_mig_interannual at stage<-charge_with_filter(object=report_mig_interannual at stage,report_mig_interannual at dc@dc_selectionne,report_mig_interannual at taxa@data$tax_code)
report_mig_interannual at stage<-choice_c(report_mig_interannual at stage,stage)
- # depending on objetreport the method will load data and issue a warning if data are not present
+ # depending on report_object the method will load data and issue a warning if data are not present
# this is the first step, the second verification will be done in method connect
report_mig_interannual at start_year<-charge(object=report_mig_interannual at start_year,
objectreport="report_mig_interannual")
@@ -392,7 +392,7 @@
#' calcule method for report_migInterannuelle
#'
#' Performs the calculation of seasonal coefficients for the plot(plot.type="seasonal") method. The numbers
-#' are split according to the period chosen, one of "day","week","month","2 weeks", french labels are also
+#' are split according to the period chosen, one of "day","week","month","2 weeks", French labels are also
#' accepted as arguments. Once this is done, the seasonality of the migration is displayed using the day when the
#' first fish was seen, then the days (or period) corresponding to 5, 50 , 95, and 100 percent of the migration.
#' The duration of 90% of the migraton between Q5 and Q95 is also of interest.
@@ -412,7 +412,7 @@
#require(dplyr)
if (!timesplit%in%c("jour","day","month","mois","week","semaine","quinzaine","2 weeks")) stop (
stringr::str_c("timesplit should be one of :","jour ","day ","month ","mois ","week ","semaine ","month ","mois ","quinzaine ","2 weeks "))
- # back to french labels for consistency with fun_report_mig_interannual code
+ # back to French labels for consistency with fun_report_mig_interannual code
timesplit<-switch(timesplit,"day"="jour_365","jour"="jour_365","week"="semaine","month"="mois","2 weeks"="quinzaine",timesplit)
# there should be just one station, this will be tested
station<-report_mig_interannual at dc@station
@@ -543,7 +543,7 @@
#' @param x An object of class report_migInterannuelle
#' @param plot.type Default standard
#' @param timesplit Used for plot.type barchart or dotplot, Default mois (month) other possible values are semaine (week), quinzaine (2 weeks),
-#' english values within parenthesis are also accepted.
+#' English values within parenthesis are also accepted.
#' @param silent Stops displaying the messages.
#' \itemize{
#' \item{plot.type="line": one line per daily report_mig}
@@ -564,7 +564,7 @@
report_mig_interannual <- x
if (!timesplit%in%c("jour","day","month","mois","week","semaine","month","mois","quinzaine","2 weeks")) stop (
stringr::str_c("timesplit should be one of :","jour ","day ","month ","mois ","week ","semaine ","month ","mois ","quinzaine ","2 weeks "))
- # back to french labels for consistency with fun_report_mig_interannual code
+ # back to French labels for consistency with fun_report_mig_interannual code
timesplit <- switch(timesplit,"day"="jour","week"="semaine","month"="mois","2 weeks"="quinzaine",timesplit)
# plot.type="line";require(ggplot2)
if(nrow(report_mig_interannual at data)>0){
@@ -1039,7 +1039,7 @@
#' Plot comparing the migration to the migration
#' computed for all years available in the daily migration table.
-#' This function plots comparisions for periods of 1 week, 2 weeks, month
+#' This function plots comparisons for periods of 1 week, 2 weeks, month
#' @param h A handler
#' @param ... Additional parameters
#' @keywords internal
@@ -1055,8 +1055,8 @@
-#' Function displaying comparaison similar to \link{hgraph_report_mig_interannual4} but using pointrange and geom_bar
-#' This function plots comparisions for periods of 1 week, 2 weeks, month
+#' Function displaying comparison similar to \link{hgraph_report_mig_interannual4} but using pointrange and geom_bar
+#' This function plots comparisons for periods of 1 week, 2 weeks, month
#' @param h A handler
#' @param ... Additional parameters
#' @keywords internal
Modified: pkg/stacomir/R/report_mig_mult.R
===================================================================
--- pkg/stacomir/R/report_mig_mult.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_mig_mult.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -197,7 +197,7 @@
#' \item{contient_poids}{A boolean which indicates, in the case of glass eel, that the function \link{fun_weight_conversion} has been run to convert the weights to numbers using the weight
#' to number coefficients in the database (see link{report_ge_weight}).}
#' \item{negative}{A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers,
-#' not developped yet}}
+#' not developed yet}}
#' @aliases calcule.report_mig_mult
#' @export
setMethod("calcule",signature=signature("report_mig_mult"),definition=function(object,negative=FALSE,silent=FALSE){
@@ -368,7 +368,7 @@
-#' handler for graphe method in report_mig_mult class
+#' handler for plot method in report_mig_mult class
#'
#' internal use
#' @param h a handler
@@ -426,9 +426,6 @@
taxa=lestaxa[taxanum,"tax_nom_latin"]
stage=lesstage[stagenum,"std_libelle"]
dc=lesdc[dcnum]
- #print(paste(taxa,stage,dc))
- # preparation du jeu de donnees pour la fonction fungraph_civ
- #developpee pour la classe report_mig
data<-report_mig_mult at calcdata[[stringr::str_c("dc_",dc)]][["data"]]
data<-data[data$lot_tax_code==lestaxa[taxanum,"tax_code"] &
data$lot_std_code==lesstage[stagenum,"std_code"],]
@@ -638,7 +635,7 @@
}
-#' hanler
+#' handler
#'
#' internal use
#' @param h a handler
Modified: pkg/stacomir/R/report_sample_char.R
===================================================================
--- pkg/stacomir/R/report_sample_char.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_sample_char.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -346,7 +346,7 @@
#' table function
#'
#' funtablereport_sample_char shows a table of results in gdf
-#' @param h hanlder passed by the graphical interface
+#' @param h handler passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @keywords internal
Modified: pkg/stacomir/R/report_sea_age.R
===================================================================
--- pkg/stacomir/R/report_sea_age.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_sea_age.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -161,7 +161,7 @@
#' @param taxa '2220=Salmo salar',
#' these should match the ref.tr_taxon_tax referential table in the stacomi database, see \link{choice_c,ref_taxa-method}
#' @param stage '5','11','BEC','BER','IND'
-#' @param par Parameters chosen for the report are mesured body size (1786), mesured fork length (1785),video size (C001) and number of year at sea (A124)
+#' @param par Parameters chosen for the report are measured body size (1786), measured fork length (1785),video size (C001) and number of year at sea (A124)
#' @param horodatedebut The starting date as a character, formats like \code{\%Y-\%m-\%d} or \code{\%d-\%m-\%Y} can be used as input
#' @param horodatefin The finishing date of the report, for this class this will be used to calculate the number of daily steps.
#' @param limit1hm Size limit of a salmon for an one sea winter fish
@@ -351,10 +351,10 @@
return(result)
})
-#' Command line method to write the caracteristic "sea age" (car_par_code='A124')
+#' Command line method to write the characteristic "sea age" (car_par_code='A124')
#' into the tj_caracteristiquelot_car table in the user's scheme
#'
-#' The sea age caracteristic is calculated from the mesured or calculated size of salmon and with a size/age rule
+#' The sea age characteristic is calculated from the measured or calculated size of salmon and with a size/age rule
#' defined by the user . the name of the database is retrieved from the odbc link
#' defined in calcmig.csv
#' @param object an object of class \link{report_sea_age-class}
@@ -462,7 +462,7 @@
#' table function
#'
#' funtablereport_sea_age shows a table of results in gdf
-#' @param h hanlder passed by the graphical interface
+#' @param h handler passed by the graphical interface
#' @param ... Additional parameters
#' @author Cedric Briand \email{cedric.briand"at"eptb-vilaine.fr}
#' @keywords internal
Modified: pkg/stacomir/R/report_silver_eel.R
===================================================================
--- pkg/stacomir/R/report_silver_eel.R 2017-06-20 11:03:56 UTC (rev 402)
+++ pkg/stacomir/R/report_silver_eel.R 2017-06-20 12:43:27 UTC (rev 403)
@@ -2,7 +2,7 @@
#'
#' the report_silver_eel class is used to calculate various statistics about the silver eel run. It comprises calculation
#' of various maturation index such as Durif's stages and Pankhurst eye index. The objective is to provide standardized
-#' output to the stations monitorin the silver eel run.
+#' output to the stations monitoring the silver eel run.
#' @include create_generic.R
#' @include ref_dc.R
#' @include ref_taxa.R
@@ -725,7 +725,7 @@
#' table function
#'
#' funtablereport_silver_eel shows a table of results in gdf
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 403
More information about the Stacomir-commits
mailing list